GSM5729923: DMSO.12h B4; Homo sapiens; OTHER
Cells were either crosslinked with formaldehyde in vivo and fragmented with MNase for the standard SSiNGLe-ILM protocol, or directly used for genomic DNA extraction followed by the SSiNGLe on HMW DNA protocol. For SSiNGLe on HMW DNA, the DNA was extracted directly from K562 cells using the TIANamp Genomic DNA Kit (TIANGEN Biotech, DP304) according to the manufacturer?s protocol. One hundred nanograms of the DNA was used directly as input into the SSiNGLe-ILM protocol (https://protocolexchange.researchsquare.com/article/pex-920/v2) at the polyA-tailing step with only one modification at the Illumina library construction stage. The step 19 in the procedure corresponding to the 2nd round PCR was performed with all (instead of just the 4 µl used in the standard protocol) DNA from the 1st round PCR. The latter was purified with the 2x volume of the VAHTS DNA Clean Beads (Vazyme) before adding to the 2nd round PCR. The libraries were prepared as described here: https://protocolexchange.researchsquare.com/article/pex-920/v2